Long non-coding RNAs (LncRNAs) are transcripts greater than 200 nucleotides in length with no protein-coding capacity. In mammals, there are tens of thousands of LncRNAs transcribed specifically in different tissues and developmental stages. The tissue-specific expression patterns of LncRNAs in development and the distinct subcellular location of LncRNAs strongly suggest that their expression is under precise control (Amaral and Mattick, 2008; Dinger et al., 2008; Mercer et al., 2008). However, it remains largely unknown how LncRNAs are regulated at the level of their transcription. There is evidence that epigenetic modifications, including DNA methylation, histone modifications, and chromatin remodeling, contribute to the cell type-specific expression patterns of LncRNAs. Recent work suggests that LncRNA promoters are subject to purifying selection (Ponjavic et al., 2007), are on average more conserved than promoters of protein-coding genes (Carninci et al., 2005), and are associated with transcription factors and regulated chromatin marks (Cawley et al., 2004; Kim et al., 2005; Boyer et al., 2006; Huarte et al., 2010; Lujambio et al., 2010; Mohammad et al., 2010; Wu et al., 2010)